Electron Density Map Problem
in Jmol 11.9.29 with gzipped CCP4 map format
Eric Martz*, February 19, 2010.

This page is obsolete. Problems described on this page were misinterpreted. Please see the MORE RECENT REPORT.


DOWNLOAD THIS FILESET jmol_edm_test5.zip
Open index.html in your browser. It will work from downloaded files without changing anything.
Electron density maps are available for most PDB files from the Uppsala Electron Density Map Server. Get the map file in CCP4 format. Files used here were renamed {PDB_code}_map.ccp4. You can then display the maps in Jmol using commands in the accompanying scripts (in the downloadable package).

The Problem.

The "cutoff 1.0" isomesh in Jmol is approximately correct near the center of the unit cell. However, as one looks farther from the center, less and less of the isomesh appears. Near the edge, the isomesh is smaller, or disappears completely. This is demonstrated below, comparing Jmol's display to PyMOL's.

Problem Example 1

3hyd is a peptide of 7 amino acids at 1.0 Å resolution. It is shown at left in Jmol with the isomesh cutoff 1.0, within 2 Å of atoms (1.spt in the downloadable package).

Now we'll examine Leu7 with isomeshes at cutoffs 1.0 and 1.5.
  (2.spt)
These isomeshes near the edge of the structure can be compared with the 1.0 and 1.5 sigma isomeshes displayed from the same 3hyd_map.ccp4 file by PyMOL (snapshot below Jmol).
   


Problem Example 2

3hz7 is a single protein chain of 87 amino acids at 2.0 Å resolution. It is shown below in Jmol with the isomesh cutoff 1.0, within 2 Å of atoms (3.spt in the downloadable package). Notice that while the 1.0 sigma isomesh in PyMOL envelops most atoms, including most waters, the cutoff 1.0 isomesh in Jmol envelops only the central atoms, leaving the peripheral atoms and nearly all of the waters outside of the isomesh.
   


Water, being at the periphery of the model, dramatically illustrates the difference between the cutoff 1.0 isomesh in Jmol (4.spt) vs. the 1.0 sigma isomesh in PyMOL.